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Team:USTC Software/notebook 5
From 2010.igem.org
Contents |
Zhen Wang
May 3 ~ May 9, 2010 Write a PPT on the framework of our game, which focused on database. We came to the conclusion that the database should have the following features, quick search, links to reactions, inheritance between different parts, easy to add elements, and most of them are still suitable now(Aug, 2010).
May 10 ~ May 16, 2010 We decide to realize the database and simulation of a biological oscillator first, the model was presented in article “A synthetic oscillatory network of transcriptional regulators”, Nature 2000.
May 17 ~ Jun 6, 2010 Summarize the reactions of oscillator, learn SBML and libsbml APIs. Search biomodels.net for SBMLs on oscillator created by other people and learn from them.
Kun Jiang
May 3 ~ May 9, 2010 Study the specification document of libsbml make an attempt at developing a sbml ode solver basing on the sundials math library.
May 10 ~ May 16, 2010 After meeting difficulty of developing a sbml ode solver from scratch, We turn to the existing library. At last, soslib v1.6.0, a library covered by the LGPL license, was choose to be as a part of our software. Add simple data display function to the soslib to get curve representation of the output data. And also need be noticed is that the soslib only support sbml version 2 level 1.
May 17 ~ Jun 6, 2010 Figure out the differences between sbml version 2 level 1 specification and sbml version 2 level 4 specification. Because our database input files are based on sbml version 2 level 4.
Luojun Wang
Regular communication and seminars with wet lab team. Different plans for promoting iGAME have been made.
Shangyu Luo
May 3 ~ May 9, 2010 I have had some knowledge of SynBioSS because I made a presentation of a igem team’ work which is the developer of this software. Thus I concentrate on studying another synthetic biology software: TinkerCell
May 10 ~ May 16, 2010 read the source code of TinkerCell and place emphasis on the simulation parts. Try to detail how it operate its modeling in sequence and detect that they use ODE and some mathematic API to simulate the biological reactions.
May 17 ~ Jun 6, 2010 specify the simulation means we will apply. I have collected some information about the methods like deterministic simulation and stochastic simulation. Meanwhile, the reaction network will have three layers: molecular reaction layer, topology layer and mathematical equations layer.
Zhengda He
Study Qt4 , HTML , JavaScript , CSS and some other computer technology , to prepare for the project . When we've already decided to make a biological game , I took the charge of designing the story of the game , so I moved to it.
5.3
Zhen Wang
Write a PPT on the framework of our game, which focused on database. We came to the
conclusion that the database should have the following features, quick search, links to
reactions, inheritance between different parts, easy to add elements, and most of them are
still suitable now(Aug, 2010).
Kun Jiang
Study the specification document of libsbml make an attempt at developing a sbml ode solver
basing on the sundials math library.
Shangyu Luo
I have had some knowledge of SynBioSS because I made a presentation of a igem team’ work
which is the developer of this software. Thus I concentrate on studying another synthetic
biology software: TinkerCell
5.10
Zhen Wang
We decide to realize the database and simulation of a biological oscillator first, the model
was presented in article “A synthetic oscillatory network of transcriptional regulators”,
Nature 2000.
Kun Jiang
After meeting difficulty of developing a sbml ode solver from scratch, We turn to the
existing library. At last, soslib v1.6.0, a library covered by the LGPL license, was choose
to be as a part of our software. Add simple data display function to the soslib to get curve
representation of the output data. And also need be noticed is that the soslib only support
sbml version 2 level 1.
Shangyu Luo
Read the source code of TinkerCell and place emphasis on the simulation parts. Try to detail
how it operate its modeling in sequence and detect that they use ODE and some mathematic API
to simulate the biological reactions.
5.17
Zhen Wang
2010 Summarize the reactions of oscillator, learn SBML and libsbml APIs. Search biomodels.net
for SBMLs on oscillator created by other people and learn from them.
Kun Jiang
2010 Figure out the differences between sbml version 2 level 1 specification and sbml version
2 level 4 specification. Because our database input files are based on sbml version 2 level
4.
Luojun Wang
Regular communication and seminars with wet lab team. Different plans for promoting iGAME
have been made.
Shangyu Luo
2010 specify the simulation means we will apply. I have collected some information about the
methods like deterministic simulation and stochastic simulation. Meanwhile, the reaction
network will have three layers: molecular reaction layer, topology layer and mathematical
equations layer.
